I gave up on SpeakerWorkshop back in 97-98, though I was primarily interested in measuring with it. I bought LAUD and still use that as my primary measurement system. I never got far with the crossover design part.
If SpeakerWorkshop only allows for a z-offset, what you will have to do is to set the x and y values to zero in WinPCD and then set the z-offset. I'm a bit surprised, because I can't see any use for having only a z-offset unless you the user is not able to acquire SPL files with measured phase. There's no issue with having M-P files.
There is a separate benefit with the three measurement technique. It's possible to create an accurate model of drivers in 3-D space without measured phase if measured SPL is available. This does require that the phase can be generated.
One key point is that you _must_ use the same driver SPL files. Any alteration of these files (or different files) will in all likelihood introduce error. No change in the driver highpass/lowpass should be made once you have determined the offset. This is true for any program, including WinPCD.